Changes about metals
Post-submission clean-up
Added Water.frc discussion, improved the integrator section, added references
new updates
edits done
more revisions
added more revisions to the paper
starting to rearrange the prose after the intro.
finished removing the trajectory analysis. took out the rattle derivation. added a section concerning the creation of init files. currently working on a table of key words for the package.
fixed the makefile, and fixed some visuals on the schemes
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